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- PDB-6mqm: Vaccine-elicited NHP FP-targeting neutralizing antibody DF1W-a.01... -

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Basic information

Entry
Database: PDB / ID: 6mqm
TitleVaccine-elicited NHP FP-targeting neutralizing antibody DF1W-a.01 in complex with HIV fusion peptide (residue 512-519)
Components
  • HIV Env fusion peptide residue 512-519
  • antibody Fab heavy chain
  • antibody Fab light chain
KeywordsIMMUNE SYSTEM / HIV / neutralizing / NHP / FP / Fusion Peptide / vaccine
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.484 Å
AuthorsXu, K. / Wang, Y. / Kwong, P.D.
CitationJournal: Cell / Year: 2019
Title: Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.
Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / ...Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Gwo-Yu Chuang / Cara W Chao / Ying Gu / Alexander J Jafari / Mark K Louder / Sijy O'Dell / Ariana P Rowshan / Elise G Viox / Yiran Wang / Chang W Choi / Martin M Corcoran / Angela R Corrigan / Venkata P Dandey / Edward T Eng / Hui Geng / Kathryn E Foulds / Yicheng Guo / Young D Kwon / Bob Lin / Kevin Liu / Rosemarie D Mason / Martha C Nason / Tiffany Y Ohr / Li Ou / Reda Rawi / Edward K Sarfo / Arne Schön / John P Todd / Shuishu Wang / Hui Wei / Winston Wu / / James C Mullikin / Robert T Bailer / Nicole A Doria-Rose / Gunilla B Karlsson Hedestam / Diana G Scorpio / Julie Overbaugh / Jesse D Bloom / Bridget Carragher / Clinton S Potter / Lawrence Shapiro / Peter D Kwong / John R Mascola /
Abstract: The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be ...The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.
History
DepositionOct 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2019Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antibody Fab heavy chain
B: antibody Fab light chain
C: HIV Env fusion peptide residue 512-519
D: antibody Fab heavy chain
E: antibody Fab light chain
F: HIV Env fusion peptide residue 512-519
G: antibody Fab heavy chain
H: antibody Fab light chain
I: HIV Env fusion peptide residue 512-519
J: antibody Fab heavy chain
K: antibody Fab light chain
L: HIV Env fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)191,56312
Polymers191,56312
Non-polymers00
Water00
1
A: antibody Fab heavy chain
B: antibody Fab light chain
C: HIV Env fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,8913
Polymers47,8913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: antibody Fab heavy chain
E: antibody Fab light chain
F: HIV Env fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,8913
Polymers47,8913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: antibody Fab heavy chain
H: antibody Fab light chain
I: HIV Env fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,8913
Polymers47,8913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: antibody Fab heavy chain
K: antibody Fab light chain
L: HIV Env fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,8913
Polymers47,8913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.906, 147.933, 102.017
Angle α, β, γ (deg.)90.000, 93.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
31chain G
41chain J
12chain C
22chain F
32chain I
42chain L
13chain B
23chain E
33chain H
43chain K

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASPASPchain AAA1 - 2171 - 222
21GLNGLNASPASPchain DDD1 - 2171 - 222
31GLNGLNASPASPchain GGG1 - 2171 - 222
41GLNGLNASPASPchain JJJ1 - 2171 - 222
12ALAALAVALVALchain CCC512 - 5181 - 7
22ALAALAVALVALchain FFF512 - 5181 - 7
32ALAALAVALVALchain III512 - 5181 - 7
42ALAALAVALVALchain LLL512 - 5181 - 7
13ASPASPGLYGLYchain BBB1 - 2121 - 217
23ASPASPGLYGLYchain EEE1 - 2121 - 217
33ASPASPGLYGLYchain HHH1 - 2121 - 217
43ASPASPGLYGLYchain KKK1 - 2121 - 217

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
antibody Fab heavy chain


Mass: 23639.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody
antibody Fab light chain


Mass: 23665.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein/peptide
HIV Env fusion peptide residue 512-519


Mass: 585.694 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KSCN and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.484→50 Å / Num. obs: 27904 / % possible obs: 96.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 65.59 Å2 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.133 / Rrim(I) all: 0.246 / Χ2: 1.027 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.563.30.56113770.7670.3590.6690.62398
3.56-3.633.30.52714220.7450.3370.6280.6897.7
3.63-3.693.30.50413990.7220.3250.6020.71797.7
3.69-3.773.30.41113920.8260.2620.4890.79997.1
3.77-3.853.20.40713990.8040.2620.4860.80497.9
3.85-3.943.20.33414050.8420.2210.4020.83397.8
3.94-4.043.20.32113930.8720.2130.3870.88297.5
4.04-4.1530.28813610.8740.1970.3510.96995.5
4.15-4.272.80.24412770.9160.1720.31.09186.5
4.27-4.412.90.22213110.930.1550.2721.28494.1
4.41-4.573.40.19114040.9540.1210.2271.15898
4.57-4.753.60.18314510.9490.1140.2161.25398.9
4.75-4.973.50.1714050.9560.1060.2011.30898.7
4.97-5.233.50.16714400.9640.1040.1981.22199.2
5.23-5.553.50.16214290.9620.1010.1921.17299.4
5.55-5.983.40.16314550.960.1030.1941.03199.3
5.98-6.583.30.15314130.9560.0980.1830.9999.1
6.58-7.533.20.13114150.9740.0850.1571.04197.8
7.53-9.483.10.08213010.9880.0550.11.24389.2
9.48-503.30.07214550.9890.0460.0861.3897.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 3.484→43.517 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1408 5.05 %
Rwork0.2002 26463 -
obs0.2025 27871 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.91 Å2 / Biso mean: 60.7222 Å2 / Biso min: 22.03 Å2
Refinement stepCycle: final / Resolution: 3.484→43.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13480 0 0 0 13480
Num. residues----1784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2676X-RAY DIFFRACTION4.9TORSIONAL
12D2676X-RAY DIFFRACTION4.9TORSIONAL
13G2676X-RAY DIFFRACTION4.9TORSIONAL
14J2676X-RAY DIFFRACTION4.9TORSIONAL
21C2612X-RAY DIFFRACTION4.9TORSIONAL
22F2612X-RAY DIFFRACTION4.9TORSIONAL
23I2612X-RAY DIFFRACTION4.9TORSIONAL
24L2612X-RAY DIFFRACTION4.9TORSIONAL
31B72X-RAY DIFFRACTION4.9TORSIONAL
32E72X-RAY DIFFRACTION4.9TORSIONAL
33H72X-RAY DIFFRACTION4.9TORSIONAL
34K72X-RAY DIFFRACTION4.9TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4842-3.60860.28811280.25242326245484
3.6086-3.75310.30781460.24832687283397
3.7531-3.92380.31491240.23772692281698
3.9238-4.13050.27831280.21852695282397
4.1305-4.3890.22911520.19242465261790
4.389-4.72750.23441390.17672736287599
4.7275-5.20260.1871570.16642723288099
5.2026-5.95380.23631570.18992762291999
5.9538-7.49490.25731410.20132724286598
7.4949-43.52070.22491360.18452653278993

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